Starting phenix.real_space_refine on Sun Feb 18 04:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aln_11818/02_2024/7aln_11818_updated.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.095 sd= 1.311 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 11 5.49 5 Mg 5 5.21 5 S 111 5.16 5 C 13157 2.51 5 N 3502 2.21 5 O 4000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 699": "NH1" <-> "NH2" Residue "F TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20789 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 6058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6058 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 740} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.79, per 1000 atoms: 0.52 Number of scatterers: 20789 At special positions: 0 Unit cell: (144.9, 126.27, 191.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 111 16.00 P 11 15.00 Mg 5 11.99 O 4000 8.00 N 3502 7.00 C 13157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 258 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 258 " distance=2.05 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 258 " distance=2.05 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 258 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 258 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 4.1 seconds 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 31 sheets defined 40.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.904A pdb=" N TYR A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 360 through 372 Proline residue: A 368 - end of helix removed outlier: 5.048A pdb=" N VAL A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.904A pdb=" N TYR B 295 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 360 through 372 Proline residue: B 368 - end of helix removed outlier: 5.047A pdb=" N VAL B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 204 through 217 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.904A pdb=" N TYR C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 339 through 348 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 360 through 372 Proline residue: C 368 - end of helix removed outlier: 5.047A pdb=" N VAL C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.904A pdb=" N TYR D 295 " --> pdb=" O LYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 360 through 372 Proline residue: D 368 - end of helix removed outlier: 5.047A pdb=" N VAL D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS D 372 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 114 through 126 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 204 through 217 Processing helix chain 'E' and resid 224 through 231 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.904A pdb=" N TYR E 295 " --> pdb=" O LYS E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 339 through 348 Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 360 through 372 Proline residue: E 368 - end of helix removed outlier: 5.047A pdb=" N VAL E 371 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS E 372 " --> pdb=" O PRO E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 148 through 156 Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 197 through 209 Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 228 through 235 Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 299 through 305 Processing helix chain 'F' and resid 331 through 340 Processing helix chain 'F' and resid 346 through 364 removed outlier: 3.980A pdb=" N ASN F 364 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 400 through 408 Processing helix chain 'F' and resid 425 through 455 removed outlier: 3.745A pdb=" N ARG F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 455 " --> pdb=" O LEU F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 511 Processing helix chain 'F' and resid 516 through 518 No H-bonds generated for 'chain 'F' and resid 516 through 518' Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'F' and resid 538 through 547 Processing helix chain 'F' and resid 554 through 563 Processing helix chain 'F' and resid 598 through 601 No H-bonds generated for 'chain 'F' and resid 598 through 601' Processing helix chain 'F' and resid 607 through 614 removed outlier: 3.680A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 641 through 657 Processing helix chain 'F' and resid 680 through 689 Processing helix chain 'F' and resid 692 through 699 Processing helix chain 'F' and resid 709 through 715 Processing helix chain 'F' and resid 721 through 724 No H-bonds generated for 'chain 'F' and resid 721 through 724' Processing helix chain 'F' and resid 731 through 741 Processing helix chain 'F' and resid 760 through 766 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 39 Processing sheet with id= C, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.598A pdb=" N TYR A 134 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 163 through 167 Processing sheet with id= E, first strand: chain 'A' and resid 239 through 242 Processing sheet with id= F, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= G, first strand: chain 'B' and resid 36 through 39 Processing sheet with id= H, first strand: chain 'B' and resid 104 through 108 removed outlier: 3.598A pdb=" N TYR B 134 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 163 through 167 Processing sheet with id= J, first strand: chain 'B' and resid 239 through 242 Processing sheet with id= K, first strand: chain 'C' and resid 9 through 13 Processing sheet with id= L, first strand: chain 'C' and resid 36 through 39 Processing sheet with id= M, first strand: chain 'C' and resid 104 through 108 removed outlier: 3.598A pdb=" N TYR C 134 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 163 through 167 Processing sheet with id= O, first strand: chain 'C' and resid 239 through 242 Processing sheet with id= P, first strand: chain 'D' and resid 9 through 13 Processing sheet with id= Q, first strand: chain 'D' and resid 36 through 39 Processing sheet with id= R, first strand: chain 'D' and resid 104 through 108 removed outlier: 3.599A pdb=" N TYR D 134 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 163 through 167 Processing sheet with id= T, first strand: chain 'D' and resid 239 through 242 Processing sheet with id= U, first strand: chain 'E' and resid 9 through 13 Processing sheet with id= V, first strand: chain 'E' and resid 36 through 39 Processing sheet with id= W, first strand: chain 'E' and resid 104 through 108 removed outlier: 3.598A pdb=" N TYR E 134 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 163 through 167 Processing sheet with id= Y, first strand: chain 'E' and resid 239 through 242 Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 38 removed outlier: 6.556A pdb=" N VAL F 56 " --> pdb=" O GLN F 70 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN F 70 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 133 through 138 removed outlier: 9.736A pdb=" N ILE F 134 " --> pdb=" O PRO F 661 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE F 663 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA F 136 " --> pdb=" O PHE F 663 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG F 665 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN F 138 " --> pdb=" O ARG F 665 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE F 667 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 250 " --> pdb=" O ASP F 469 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR F 264 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 367 through 369 Processing sheet with id= AC, first strand: chain 'F' and resid 409 through 413 Processing sheet with id= AD, first strand: chain 'F' and resid 570 through 572 Processing sheet with id= AE, first strand: chain 'F' and resid 705 through 708 744 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5648 1.33 - 1.46: 5913 1.46 - 1.60: 9460 1.60 - 1.73: 1 1.73 - 1.86: 192 Bond restraints: 21214 Sorted by residual: bond pdb=" C4 9UE A 403 " pdb=" C5 9UE A 403 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.52e+02 bond pdb=" C4 9UE E 403 " pdb=" C5 9UE E 403 " ideal model delta sigma weight residual 0.880 1.496 -0.616 2.00e-02 2.50e+03 9.50e+02 bond pdb=" C4 9UE C 403 " pdb=" C5 9UE C 403 " ideal model delta sigma weight residual 0.880 1.496 -0.616 2.00e-02 2.50e+03 9.47e+02 bond pdb=" C11 9UE C 403 " pdb=" C12 9UE C 403 " ideal model delta sigma weight residual 2.064 1.513 0.551 2.00e-02 2.50e+03 7.59e+02 bond pdb=" C11 9UE E 403 " pdb=" C12 9UE E 403 " ideal model delta sigma weight residual 2.064 1.514 0.550 2.00e-02 2.50e+03 7.57e+02 ... (remaining 21209 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.86: 442 104.86 - 112.74: 11295 112.74 - 120.62: 10009 120.62 - 128.50: 6839 128.50 - 136.38: 143 Bond angle restraints: 28728 Sorted by residual: angle pdb=" C20 9UE C 403 " pdb=" C21 9UE C 403 " pdb=" C28 9UE C 403 " ideal model delta sigma weight residual 73.46 128.40 -54.94 3.00e+00 1.11e-01 3.35e+02 angle pdb=" C20 9UE E 403 " pdb=" C21 9UE E 403 " pdb=" C28 9UE E 403 " ideal model delta sigma weight residual 73.46 128.39 -54.93 3.00e+00 1.11e-01 3.35e+02 angle pdb=" C20 9UE A 403 " pdb=" C21 9UE A 403 " pdb=" C28 9UE A 403 " ideal model delta sigma weight residual 73.46 128.35 -54.89 3.00e+00 1.11e-01 3.35e+02 angle pdb=" C20 9UE C 403 " pdb=" C21 9UE C 403 " pdb=" C22 9UE C 403 " ideal model delta sigma weight residual 176.54 125.66 50.88 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C20 9UE E 403 " pdb=" C21 9UE E 403 " pdb=" C22 9UE E 403 " ideal model delta sigma weight residual 176.54 125.66 50.88 3.00e+00 1.11e-01 2.88e+02 ... (remaining 28723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 12698 34.85 - 69.71: 52 69.71 - 104.56: 8 104.56 - 139.41: 23 139.41 - 174.27: 21 Dihedral angle restraints: 12802 sinusoidal: 5273 harmonic: 7529 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.73 174.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.84 174.16 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 128.00 172.00 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 12799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3046 0.122 - 0.243: 147 0.243 - 0.365: 1 0.365 - 0.486: 3 0.486 - 0.608: 3 Chirality restraints: 3200 Sorted by residual: chirality pdb=" C6 9UE A 403 " pdb=" N 9UE A 403 " pdb=" C29 9UE A 403 " pdb=" C5 9UE A 403 " both_signs ideal model delta sigma weight residual False -2.65 -2.04 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C6 9UE E 403 " pdb=" N 9UE E 403 " pdb=" C29 9UE E 403 " pdb=" C5 9UE E 403 " both_signs ideal model delta sigma weight residual False -2.65 -2.04 -0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" C6 9UE C 403 " pdb=" N 9UE C 403 " pdb=" C29 9UE C 403 " pdb=" C5 9UE C 403 " both_signs ideal model delta sigma weight residual False -2.65 -2.05 -0.60 2.00e-01 2.50e+01 9.05e+00 ... (remaining 3197 not shown) Planarity restraints: 3677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 9UE C 403 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C11 9UE C 403 " 0.045 2.00e-02 2.50e+03 pdb=" C12 9UE C 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 9UE C 403 " 0.302 2.00e-02 2.50e+03 pdb=" O4 9UE C 403 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9UE E 403 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C11 9UE E 403 " 0.047 2.00e-02 2.50e+03 pdb=" C12 9UE E 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 9UE E 403 " 0.302 2.00e-02 2.50e+03 pdb=" O4 9UE E 403 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9UE A 403 " -0.216 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C11 9UE A 403 " 0.047 2.00e-02 2.50e+03 pdb=" C12 9UE A 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 9UE A 403 " 0.301 2.00e-02 2.50e+03 pdb=" O4 9UE A 403 " 0.014 2.00e-02 2.50e+03 ... (remaining 3674 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 84 2.43 - 3.04: 12140 3.04 - 3.66: 31081 3.66 - 4.28: 49410 4.28 - 4.90: 80483 Nonbonded interactions: 173198 Sorted by model distance: nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.807 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.837 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.957 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.013 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.053 2.170 ... (remaining 173193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 375 or resid 401 through 402)) selection = chain 'B' selection = (chain 'C' and (resid 6 through 375 or resid 401 through 402)) selection = chain 'D' selection = (chain 'E' and (resid 6 through 375 or resid 401 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.840 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 55.790 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.617 21214 Z= 1.211 Angle : 1.653 54.941 28728 Z= 0.696 Chirality : 0.064 0.608 3200 Planarity : 0.009 0.180 3677 Dihedral : 14.080 174.267 7959 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 0.22 % Allowed : 1.86 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.13), residues: 2599 helix: -3.04 (0.09), residues: 1072 sheet: -2.64 (0.23), residues: 386 loop : -1.97 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP B 341 HIS 0.015 0.003 HIS B 195 PHE 0.031 0.003 PHE F 444 TYR 0.031 0.003 TYR C 189 ARG 0.017 0.001 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 543 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 218 CYS cc_start: 0.5965 (m) cc_final: 0.5671 (m) REVERT: A 228 MET cc_start: 0.8537 (mmm) cc_final: 0.8185 (tpp) REVERT: B 55 VAL cc_start: 0.9461 (t) cc_final: 0.9145 (p) REVERT: B 206 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 208 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 228 MET cc_start: 0.8603 (mmm) cc_final: 0.8382 (tpp) REVERT: C 191 MET cc_start: 0.8159 (mtm) cc_final: 0.7881 (mtp) REVERT: C 284 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8661 (mtpp) REVERT: C 306 MET cc_start: 0.8656 (mmm) cc_final: 0.8365 (mmt) REVERT: D 45 MET cc_start: 0.8243 (mmm) cc_final: 0.7992 (tpt) REVERT: D 70 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: D 83 MET cc_start: 0.8529 (tpt) cc_final: 0.8123 (tpt) REVERT: D 144 TYR cc_start: 0.8392 (m-80) cc_final: 0.8188 (m-80) REVERT: D 228 MET cc_start: 0.8539 (mmm) cc_final: 0.8263 (tpp) REVERT: E 228 MET cc_start: 0.8530 (mmm) cc_final: 0.7968 (tpp) REVERT: E 356 MET cc_start: 0.8696 (mtt) cc_final: 0.8470 (mtm) REVERT: F 47 ASP cc_start: 0.5421 (t0) cc_final: 0.5217 (m-30) REVERT: F 368 ILE cc_start: 0.8547 (pt) cc_final: 0.8254 (mm) REVERT: F 445 LEU cc_start: 0.8290 (mt) cc_final: 0.7814 (mt) REVERT: F 555 LYS cc_start: 0.7535 (mttt) cc_final: 0.7314 (mttt) REVERT: F 568 ASN cc_start: 0.7649 (p0) cc_final: 0.7214 (t0) REVERT: F 694 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7011 (tp30) REVERT: F 699 ARG cc_start: 0.6529 (tpt170) cc_final: 0.5771 (ttm-80) REVERT: F 714 TYR cc_start: 0.8331 (t80) cc_final: 0.8089 (t80) outliers start: 5 outliers final: 0 residues processed: 548 average time/residue: 0.3783 time to fit residues: 304.9069 Evaluate side-chains 286 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN B 74 HIS ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 297 ASN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN F 91 ASN F 182 ASN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN F 288 HIS F 292 GLN F 341 ASN F 450 HIS ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21214 Z= 0.350 Angle : 0.997 47.924 28728 Z= 0.421 Chirality : 0.048 0.315 3200 Planarity : 0.005 0.055 3677 Dihedral : 17.056 179.024 2925 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.01 % Allowed : 6.90 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2599 helix: -0.91 (0.14), residues: 1077 sheet: -2.43 (0.24), residues: 388 loop : -1.45 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 341 HIS 0.008 0.001 HIS F 288 PHE 0.025 0.002 PHE F 476 TYR 0.020 0.002 TYR F 207 ARG 0.005 0.001 ARG F 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 295 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 188 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: B 55 VAL cc_start: 0.9445 (t) cc_final: 0.9115 (p) REVERT: B 133 MET cc_start: 0.9009 (tmm) cc_final: 0.8699 (tmm) REVERT: B 206 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7013 (mp0) REVERT: C 177 MET cc_start: 0.7796 (mtm) cc_final: 0.7555 (mtp) REVERT: C 212 ASP cc_start: 0.8910 (t0) cc_final: 0.8673 (t70) REVERT: C 228 MET cc_start: 0.8571 (mmm) cc_final: 0.8331 (tpp) REVERT: C 284 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8807 (mtpp) REVERT: C 326 MET cc_start: 0.7913 (ttm) cc_final: 0.7565 (ttp) REVERT: D 45 MET cc_start: 0.8552 (mmm) cc_final: 0.8150 (tpt) REVERT: D 83 MET cc_start: 0.8581 (tpt) cc_final: 0.8275 (tmm) REVERT: D 228 MET cc_start: 0.8535 (mmm) cc_final: 0.8181 (tpp) REVERT: D 271 GLU cc_start: 0.7418 (tt0) cc_final: 0.6988 (tm-30) REVERT: E 133 MET cc_start: 0.8999 (tmm) cc_final: 0.8604 (tmm) REVERT: E 212 ASP cc_start: 0.8713 (t0) cc_final: 0.8134 (t0) REVERT: F 216 MET cc_start: 0.2056 (OUTLIER) cc_final: 0.0532 (mmp) REVERT: F 355 ILE cc_start: 0.8411 (mt) cc_final: 0.8137 (mt) REVERT: F 445 LEU cc_start: 0.8622 (mt) cc_final: 0.7751 (mm) REVERT: F 568 ASN cc_start: 0.7726 (p0) cc_final: 0.7323 (t0) REVERT: F 683 ILE cc_start: 0.8492 (mt) cc_final: 0.8290 (pt) REVERT: F 694 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7331 (tp30) REVERT: F 699 ARG cc_start: 0.7040 (tpt170) cc_final: 0.6269 (ttm-80) REVERT: F 714 TYR cc_start: 0.8363 (t80) cc_final: 0.8125 (t80) outliers start: 68 outliers final: 42 residues processed: 343 average time/residue: 0.3270 time to fit residues: 173.0465 Evaluate side-chains 266 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 467 MET Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 74 HIS ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 276 HIS D 74 HIS ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 74 HIS ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 70 GLN F 177 ASN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN F 253 GLN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 21214 Z= 0.560 Angle : 1.072 47.154 28728 Z= 0.468 Chirality : 0.052 0.219 3200 Planarity : 0.005 0.052 3677 Dihedral : 17.078 178.639 2923 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.76 % Allowed : 10.12 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2599 helix: -0.69 (0.15), residues: 1115 sheet: -2.24 (0.23), residues: 393 loop : -1.46 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 341 HIS 0.011 0.002 HIS A 162 PHE 0.026 0.002 PHE F 208 TYR 0.019 0.002 TYR F 207 ARG 0.008 0.001 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 236 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 34 SER cc_start: 0.9263 (m) cc_final: 0.9062 (p) REVERT: A 188 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: B 133 MET cc_start: 0.9030 (tmm) cc_final: 0.8698 (tmm) REVERT: B 188 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 206 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7167 (mp0) REVERT: C 212 ASP cc_start: 0.8960 (t0) cc_final: 0.8722 (t70) REVERT: C 228 MET cc_start: 0.8541 (mmm) cc_final: 0.8299 (tpp) REVERT: C 284 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8971 (mtpp) REVERT: C 292 LYS cc_start: 0.6026 (mptt) cc_final: 0.5711 (mmtt) REVERT: C 326 MET cc_start: 0.7454 (ttm) cc_final: 0.7047 (ttm) REVERT: D 45 MET cc_start: 0.8669 (mmm) cc_final: 0.8363 (tpt) REVERT: D 188 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: D 206 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7017 (mp0) REVERT: D 228 MET cc_start: 0.8533 (mmm) cc_final: 0.8287 (tpp) REVERT: D 271 GLU cc_start: 0.7515 (tt0) cc_final: 0.7096 (tm-30) REVERT: E 133 MET cc_start: 0.8912 (tmm) cc_final: 0.8528 (tmm) REVERT: E 188 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: F 386 MET cc_start: 0.6933 (mmm) cc_final: 0.6486 (tpp) REVERT: F 568 ASN cc_start: 0.7798 (p0) cc_final: 0.7471 (t0) REVERT: F 676 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6334 (tp) REVERT: F 683 ILE cc_start: 0.8514 (mt) cc_final: 0.8282 (pt) REVERT: F 694 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7414 (tp30) REVERT: F 699 ARG cc_start: 0.7205 (tpt170) cc_final: 0.5925 (tpt-90) REVERT: F 714 TYR cc_start: 0.8469 (t80) cc_final: 0.8140 (t80) outliers start: 85 outliers final: 52 residues processed: 307 average time/residue: 0.3202 time to fit residues: 154.9878 Evaluate side-chains 253 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 221 GLN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21214 Z= 0.172 Angle : 0.916 47.192 28728 Z= 0.370 Chirality : 0.044 0.240 3200 Planarity : 0.004 0.049 3677 Dihedral : 16.240 176.810 2923 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.72 % Allowed : 12.95 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2599 helix: 0.31 (0.16), residues: 1081 sheet: -1.54 (0.23), residues: 433 loop : -1.10 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 341 HIS 0.008 0.001 HIS A 162 PHE 0.033 0.001 PHE F 208 TYR 0.011 0.001 TYR F 80 ARG 0.007 0.001 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 240 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 34 SER cc_start: 0.9197 (m) cc_final: 0.8958 (p) REVERT: A 188 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: B 55 VAL cc_start: 0.9353 (t) cc_final: 0.8966 (p) REVERT: B 188 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 206 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6766 (mp0) REVERT: C 152 ILE cc_start: 0.9007 (mt) cc_final: 0.8719 (mt) REVERT: C 212 ASP cc_start: 0.8889 (t0) cc_final: 0.8425 (t0) REVERT: C 292 LYS cc_start: 0.5996 (mptt) cc_final: 0.5600 (mmtt) REVERT: C 326 MET cc_start: 0.7389 (ttm) cc_final: 0.7092 (ttm) REVERT: D 45 MET cc_start: 0.8457 (mmm) cc_final: 0.8171 (tpt) REVERT: D 206 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6900 (mp0) REVERT: D 228 MET cc_start: 0.8497 (mmm) cc_final: 0.8225 (tpp) REVERT: E 133 MET cc_start: 0.8978 (tmm) cc_final: 0.8751 (tmm) REVERT: E 188 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: F 193 SER cc_start: 0.7243 (OUTLIER) cc_final: 0.6818 (t) REVERT: F 234 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6592 (t80) REVERT: F 516 THR cc_start: 0.6184 (m) cc_final: 0.5755 (t) REVERT: F 525 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7632 (pttm) REVERT: F 555 LYS cc_start: 0.7149 (mtpt) cc_final: 0.6881 (mttt) REVERT: F 568 ASN cc_start: 0.7619 (p0) cc_final: 0.7225 (t0) REVERT: F 714 TYR cc_start: 0.8413 (t80) cc_final: 0.8147 (t80) outliers start: 39 outliers final: 21 residues processed: 271 average time/residue: 0.3411 time to fit residues: 142.9439 Evaluate side-chains 234 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 643 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 HIS ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21214 Z= 0.396 Angle : 0.986 47.077 28728 Z= 0.414 Chirality : 0.048 0.225 3200 Planarity : 0.004 0.049 3677 Dihedral : 16.395 179.704 2923 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.14 % Allowed : 13.22 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2599 helix: 0.10 (0.15), residues: 1120 sheet: -1.98 (0.23), residues: 389 loop : -1.13 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 341 HIS 0.010 0.001 HIS A 162 PHE 0.025 0.002 PHE F 208 TYR 0.015 0.001 TYR F 121 ARG 0.005 0.001 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 203 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: A 271 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6638 (tm-30) REVERT: B 133 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8772 (ppp) REVERT: B 188 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: B 271 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6809 (tm-30) REVERT: C 152 ILE cc_start: 0.9002 (mt) cc_final: 0.8783 (mt) REVERT: C 212 ASP cc_start: 0.8958 (t0) cc_final: 0.8710 (t70) REVERT: C 292 LYS cc_start: 0.6004 (mptt) cc_final: 0.5597 (mmtt) REVERT: C 326 MET cc_start: 0.7343 (ttm) cc_final: 0.6977 (ttm) REVERT: D 45 MET cc_start: 0.8553 (mmm) cc_final: 0.8220 (tpt) REVERT: D 228 MET cc_start: 0.8481 (mmm) cc_final: 0.8219 (tpp) REVERT: D 271 GLU cc_start: 0.7741 (tt0) cc_final: 0.7288 (tm-30) REVERT: E 133 MET cc_start: 0.8899 (tmm) cc_final: 0.8547 (tmm) REVERT: E 206 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6979 (mp0) REVERT: E 228 MET cc_start: 0.8518 (tpp) cc_final: 0.8173 (mpp) REVERT: F 234 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6523 (t80) REVERT: F 525 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7916 (pttm) REVERT: F 555 LYS cc_start: 0.7363 (mtpt) cc_final: 0.7159 (mttt) REVERT: F 568 ASN cc_start: 0.7680 (p0) cc_final: 0.7341 (t0) REVERT: F 699 ARG cc_start: 0.7136 (tpt170) cc_final: 0.6491 (tpt-90) REVERT: F 714 TYR cc_start: 0.8527 (t80) cc_final: 0.8252 (t80) outliers start: 71 outliers final: 46 residues processed: 257 average time/residue: 0.2893 time to fit residues: 120.0851 Evaluate side-chains 238 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 252 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21214 Z= 0.324 Angle : 0.954 47.160 28728 Z= 0.392 Chirality : 0.047 0.258 3200 Planarity : 0.004 0.048 3677 Dihedral : 16.198 178.801 2923 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.92 % Allowed : 14.32 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2599 helix: 0.20 (0.15), residues: 1115 sheet: -1.37 (0.24), residues: 449 loop : -1.07 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 446 HIS 0.010 0.001 HIS A 162 PHE 0.027 0.001 PHE F 208 TYR 0.013 0.001 TYR F 80 ARG 0.005 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 202 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: A 228 MET cc_start: 0.8456 (tpp) cc_final: 0.8251 (mpp) REVERT: A 271 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6657 (tm-30) REVERT: B 188 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 271 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6858 (tm-30) REVERT: C 152 ILE cc_start: 0.8980 (mt) cc_final: 0.8759 (mt) REVERT: C 212 ASP cc_start: 0.8942 (t0) cc_final: 0.8667 (t70) REVERT: C 292 LYS cc_start: 0.5993 (mptt) cc_final: 0.5528 (mmtt) REVERT: C 326 MET cc_start: 0.7206 (ttm) cc_final: 0.6778 (ttm) REVERT: D 45 MET cc_start: 0.8560 (mmm) cc_final: 0.8234 (tpt) REVERT: D 133 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8858 (tmm) REVERT: D 206 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6791 (mp0) REVERT: D 228 MET cc_start: 0.8443 (mmm) cc_final: 0.8213 (tpp) REVERT: D 271 GLU cc_start: 0.7654 (tt0) cc_final: 0.7298 (tm-30) REVERT: E 133 MET cc_start: 0.8903 (tmm) cc_final: 0.8567 (tmm) REVERT: E 206 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6961 (mp0) REVERT: F 234 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6582 (t80) REVERT: F 516 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6029 (t) REVERT: F 525 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7725 (pttm) REVERT: F 555 LYS cc_start: 0.7312 (mtpt) cc_final: 0.7055 (mttt) REVERT: F 568 ASN cc_start: 0.7590 (p0) cc_final: 0.7253 (t0) REVERT: F 676 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6242 (tp) REVERT: F 714 TYR cc_start: 0.8534 (t80) cc_final: 0.8287 (t80) outliers start: 66 outliers final: 47 residues processed: 256 average time/residue: 0.2999 time to fit residues: 123.2833 Evaluate side-chains 240 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 186 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain F residue 597 PHE Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21214 Z= 0.240 Angle : 0.932 47.157 28728 Z= 0.377 Chirality : 0.046 0.274 3200 Planarity : 0.004 0.047 3677 Dihedral : 15.965 178.862 2923 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.61 % Allowed : 15.08 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2599 helix: 0.40 (0.16), residues: 1114 sheet: -1.24 (0.24), residues: 449 loop : -0.87 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 341 HIS 0.009 0.001 HIS A 162 PHE 0.027 0.001 PHE F 208 TYR 0.011 0.001 TYR F 121 ARG 0.004 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 198 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: B 49 GLU cc_start: 0.7820 (mp0) cc_final: 0.6893 (mm-30) REVERT: B 188 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 271 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: C 152 ILE cc_start: 0.8966 (mt) cc_final: 0.8521 (mt) REVERT: C 212 ASP cc_start: 0.8922 (t0) cc_final: 0.8630 (t70) REVERT: C 292 LYS cc_start: 0.6014 (mptt) cc_final: 0.4574 (mmtp) REVERT: C 326 MET cc_start: 0.7173 (ttm) cc_final: 0.6858 (ttm) REVERT: D 45 MET cc_start: 0.8554 (mmm) cc_final: 0.8325 (tpt) REVERT: D 133 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8923 (ppp) REVERT: D 206 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6867 (mp0) REVERT: D 228 MET cc_start: 0.8443 (mmm) cc_final: 0.8238 (tpp) REVERT: D 271 GLU cc_start: 0.7567 (tt0) cc_final: 0.7275 (tm-30) REVERT: E 133 MET cc_start: 0.8892 (tmm) cc_final: 0.8637 (tmm) REVERT: E 188 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: E 228 MET cc_start: 0.8587 (tpp) cc_final: 0.8323 (mpp) REVERT: F 110 ILE cc_start: 0.8413 (mp) cc_final: 0.8186 (mt) REVERT: F 516 THR cc_start: 0.6545 (m) cc_final: 0.6128 (t) REVERT: F 525 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7732 (pttm) REVERT: F 568 ASN cc_start: 0.7589 (p0) cc_final: 0.7379 (t0) REVERT: F 676 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6100 (tp) REVERT: F 699 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6239 (tpm170) REVERT: F 714 TYR cc_start: 0.8479 (t80) cc_final: 0.8236 (t80) outliers start: 59 outliers final: 45 residues processed: 243 average time/residue: 0.3107 time to fit residues: 121.4731 Evaluate side-chains 239 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 597 PHE Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN D 116 ASN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21214 Z= 0.200 Angle : 0.918 47.152 28728 Z= 0.367 Chirality : 0.045 0.283 3200 Planarity : 0.004 0.045 3677 Dihedral : 15.779 179.286 2923 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.87 % Allowed : 15.21 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2599 helix: 0.58 (0.16), residues: 1109 sheet: -1.17 (0.24), residues: 449 loop : -0.75 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 341 HIS 0.008 0.001 HIS A 162 PHE 0.025 0.001 PHE F 208 TYR 0.016 0.001 TYR C 295 ARG 0.004 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 201 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 49 GLU cc_start: 0.7799 (mp0) cc_final: 0.6933 (mm-30) REVERT: B 188 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: B 271 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: C 212 ASP cc_start: 0.8897 (t0) cc_final: 0.8495 (t0) REVERT: C 292 LYS cc_start: 0.6087 (mptt) cc_final: 0.4709 (mmtp) REVERT: C 326 MET cc_start: 0.7095 (ttm) cc_final: 0.6752 (ttm) REVERT: D 133 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8906 (ppp) REVERT: D 206 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6820 (mp0) REVERT: D 228 MET cc_start: 0.8470 (mmm) cc_final: 0.8216 (tpp) REVERT: D 271 GLU cc_start: 0.7649 (tt0) cc_final: 0.7289 (tm-30) REVERT: E 133 MET cc_start: 0.8893 (tmm) cc_final: 0.8677 (tmm) REVERT: E 188 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: E 212 ASP cc_start: 0.8751 (t0) cc_final: 0.8361 (t0) REVERT: E 228 MET cc_start: 0.8599 (tpp) cc_final: 0.8346 (mpp) REVERT: F 381 ILE cc_start: 0.7599 (mm) cc_final: 0.7348 (mt) REVERT: F 405 ARG cc_start: 0.8029 (mmp80) cc_final: 0.7406 (ttt90) REVERT: F 516 THR cc_start: 0.6581 (m) cc_final: 0.6148 (t) REVERT: F 532 CYS cc_start: 0.6727 (t) cc_final: 0.6456 (t) REVERT: F 568 ASN cc_start: 0.7539 (p0) cc_final: 0.7309 (t0) REVERT: F 676 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5896 (tp) REVERT: F 699 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6298 (tpm170) REVERT: F 714 TYR cc_start: 0.8443 (t80) cc_final: 0.8189 (t80) outliers start: 65 outliers final: 50 residues processed: 251 average time/residue: 0.3085 time to fit residues: 125.6789 Evaluate side-chains 249 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 193 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 597 PHE Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21214 Z= 0.293 Angle : 0.947 47.188 28728 Z= 0.387 Chirality : 0.047 0.301 3200 Planarity : 0.004 0.046 3677 Dihedral : 15.866 179.108 2923 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.92 % Allowed : 15.52 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2599 helix: 0.55 (0.16), residues: 1115 sheet: -1.15 (0.24), residues: 449 loop : -0.74 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 341 HIS 0.010 0.001 HIS A 162 PHE 0.021 0.001 PHE F 208 TYR 0.012 0.001 TYR F 121 ARG 0.004 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 194 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7029 (mp0) cc_final: 0.6303 (mm-30) REVERT: A 188 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: B 49 GLU cc_start: 0.7669 (mp0) cc_final: 0.6844 (mm-30) REVERT: B 188 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 206 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6973 (mp0) REVERT: B 212 ASP cc_start: 0.8791 (t0) cc_final: 0.8190 (t0) REVERT: B 271 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: C 81 ASP cc_start: 0.7797 (t0) cc_final: 0.7589 (t0) REVERT: C 212 ASP cc_start: 0.8930 (t0) cc_final: 0.8632 (t70) REVERT: C 292 LYS cc_start: 0.6109 (mptt) cc_final: 0.5652 (mmtt) REVERT: C 326 MET cc_start: 0.7160 (ttm) cc_final: 0.6838 (ttm) REVERT: D 133 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8899 (ppp) REVERT: D 206 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6831 (mp0) REVERT: D 228 MET cc_start: 0.8478 (mmm) cc_final: 0.8240 (tpp) REVERT: D 271 GLU cc_start: 0.7630 (tt0) cc_final: 0.7279 (tm-30) REVERT: E 133 MET cc_start: 0.8876 (tmm) cc_final: 0.8637 (tmm) REVERT: E 188 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: E 212 ASP cc_start: 0.8747 (t0) cc_final: 0.8348 (t0) REVERT: F 110 ILE cc_start: 0.8430 (mp) cc_final: 0.8201 (mt) REVERT: F 516 THR cc_start: 0.6522 (m) cc_final: 0.6101 (t) REVERT: F 525 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7642 (pttm) REVERT: F 568 ASN cc_start: 0.7451 (p0) cc_final: 0.7239 (t0) REVERT: F 676 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6058 (tp) REVERT: F 714 TYR cc_start: 0.8468 (t80) cc_final: 0.8219 (t80) outliers start: 66 outliers final: 53 residues processed: 244 average time/residue: 0.2883 time to fit residues: 113.1342 Evaluate side-chains 249 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain F residue 597 PHE Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 672 ASN Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21214 Z= 0.279 Angle : 0.948 47.215 28728 Z= 0.386 Chirality : 0.046 0.306 3200 Planarity : 0.004 0.049 3677 Dihedral : 15.875 179.596 2923 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.79 % Allowed : 15.83 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2599 helix: 0.55 (0.16), residues: 1121 sheet: -1.10 (0.24), residues: 449 loop : -0.70 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 341 HIS 0.010 0.001 HIS A 162 PHE 0.021 0.001 PHE F 208 TYR 0.012 0.001 TYR F 121 ARG 0.007 0.001 ARG A 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 194 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7020 (mp0) cc_final: 0.6316 (mm-30) REVERT: A 188 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 49 GLU cc_start: 0.7575 (mp0) cc_final: 0.6796 (mm-30) REVERT: B 188 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 212 ASP cc_start: 0.8786 (t0) cc_final: 0.8167 (t0) REVERT: B 271 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: C 81 ASP cc_start: 0.7792 (t0) cc_final: 0.7575 (t0) REVERT: C 212 ASP cc_start: 0.8917 (t0) cc_final: 0.8514 (t0) REVERT: C 271 GLU cc_start: 0.3391 (OUTLIER) cc_final: 0.1819 (pp20) REVERT: C 292 LYS cc_start: 0.6076 (mptt) cc_final: 0.5652 (mmtt) REVERT: C 326 MET cc_start: 0.7145 (ttm) cc_final: 0.6802 (ttm) REVERT: D 133 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8894 (ppp) REVERT: D 206 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6777 (mp0) REVERT: D 228 MET cc_start: 0.8445 (mmm) cc_final: 0.8207 (tpp) REVERT: D 271 GLU cc_start: 0.7723 (tt0) cc_final: 0.7348 (tm-30) REVERT: E 45 MET cc_start: 0.8078 (mtp) cc_final: 0.7861 (mtp) REVERT: E 188 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: E 212 ASP cc_start: 0.8724 (t0) cc_final: 0.8333 (t0) REVERT: F 114 LEU cc_start: 0.7874 (tt) cc_final: 0.7670 (mp) REVERT: F 405 ARG cc_start: 0.7889 (mmp80) cc_final: 0.7300 (ttt90) REVERT: F 516 THR cc_start: 0.6559 (m) cc_final: 0.6128 (t) REVERT: F 525 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7721 (pttm) REVERT: F 532 CYS cc_start: 0.6908 (t) cc_final: 0.6659 (t) REVERT: F 676 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6037 (tp) REVERT: F 714 TYR cc_start: 0.8468 (t80) cc_final: 0.8217 (t80) outliers start: 63 outliers final: 54 residues processed: 245 average time/residue: 0.2913 time to fit residues: 116.2420 Evaluate side-chains 252 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 190 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 597 PHE Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 672 ASN Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 63 optimal weight: 0.0270 chunk 190 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 212 optimal weight: 20.0000 chunk 26 optimal weight: 0.0470 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 116 ASN B 116 ASN E 41 ASN E 116 ASN F 70 GLN F 166 HIS ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.080730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064666 restraints weight = 57013.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066661 restraints weight = 28216.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067983 restraints weight = 16655.251| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21214 Z= 0.151 Angle : 0.917 47.189 28728 Z= 0.365 Chirality : 0.044 0.290 3200 Planarity : 0.004 0.052 3677 Dihedral : 15.493 178.626 2923 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 16.76 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2599 helix: 1.10 (0.16), residues: 1066 sheet: -1.00 (0.25), residues: 432 loop : -0.44 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 341 HIS 0.007 0.001 HIS A 162 PHE 0.024 0.001 PHE F 208 TYR 0.017 0.001 TYR F 521 ARG 0.005 0.000 ARG F 366 =============================================================================== Job complete usr+sys time: 3855.86 seconds wall clock time: 71 minutes 39.97 seconds (4299.97 seconds total)